PlantTFDB
PlantRegMap/PlantTFDB v5.0
Plant Transcription Factor Database
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(e.g., LFY)
Transcription Factor Information
Basic Information | Signature Domain | Sequence | 
Basic Information? help Back to Top
TF ID Potri.001G189200.2
Common NamePOPTR_0001s19000g
Organism
Populus trichocarpa
Taxonomic ID
Taxonomic Lineage
cellular organisms; Eukaryota; Viridiplantae; Streptophyta; Streptophytina; Embryophyta; Tracheophyta; Euphyllophyta; Spermatophyta; Magnoliophyta; Mesangiospermae; eudicotyledons; Gunneridae; Pentapetalae; rosids; fabids; Malpighiales; Salicaceae; Saliceae; Populus
Family HB-other
Protein Properties Length: 190aa    MW: 21786.7 Da    PI: 5.0305
Description HB-other family protein
Gene Model
Gene Model ID Type Source Coding Sequence
Potri.001G189200.2genomeJGIView CDS
Signature Domain? help Back to Top
Signature Domain
No. Domain Score E-value Start End HMM Start HMM End
1Homeobox16.81.2e-05561751
                        --HHHHHHHHHHHHH..SSS--HHHHHHHHHHC..........TS-HHHHHHHHHHH CS
            Homeobox  7 ftkeqleeLeelFek..nrypsaeereeLAkkl..........gLterqVkvWFqNr 51
                        ft ++  e+e++F++  +  +  +  e+LA++            +t rqVk WFq r
  Potri.001G189200.2  5 FTLSEMLEMENMFKEleEGPLAPQFCEKLASSFslapsrdgkqAITPRQVKSWFQDR 61
                        7888999*******8735555666689*****999********************88 PP
Protein Features ? help Back to Top
3D Structure
Database Entry ID E-value Start End InterPro ID Description
PROSITE profilePS500718.989168IPR001356Homeobox domain
Gene3DG3DSA:1.10.10.600.001564IPR009057Homeodomain-like
PfamPF167191.6E-2799184IPR032001SAWADEE domain
Gene Ontology ? help Back to Top
GO Term GO Category GO Description
GO:0006306Biological ProcessDNA methylation
GO:0006346Biological Processmethylation-dependent chromatin silencing
GO:0031047Biological Processgene silencing by RNA
GO:0003677Molecular FunctionDNA binding
GO:0003682Molecular Functionchromatin binding
Sequence ? help Back to Top
Protein Sequence    Length: 190 aa     Download sequence    Send to blast
MDFEFTLSEM LEMENMFKEL EEGPLAPQFC EKLASSFSLA PSRDGKQAIT PRQVKSWFQD  60
RLKKSQPRVA SSNMALKLFA DLSDASASFG ATESSQKLKD DEWVNVRRAV RERSIPLESS  120
ECQRVKVGDL VLCFQEREER AVYCDAHIVE INRKLHDING CRCTFVVRYD HDDFEEEVRL  180
DRLCGRPTP*
3D Structure ? help Back to Top
Structure
PDB ID Evalue Query Start Query End Hit Start Hit End Description
4iup_A5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
4iup_B5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_A5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuq_B5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
4iur_A5e-349918745133SHH1 SAWADEE
4iur_B5e-349918745133SHH1 SAWADEE
4iut_A5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
4iut_B5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_A5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuu_B5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_A5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
4iuv_B5e-349918745133SAWADEE HOMEODOMAIN HOMOLOG 1
Search in ModeBase
Functional Description ? help Back to Top
Source Description
UniProtInvolved in RNA-directed DNA methylation (RdDM). Required for the silencing of some endogenous RdDM targets and accumulation of 24-nt siRNAs, but not for the production of Pol V-dependent transcripts. Functions in transcriptional silencing through both DNA methylation-dependent and -independent pathways. Required for both maintenance and de-novo DNA methylation. Plays a role in the recruitment of Pol IV to genomic regions associated with K9 methylated histone H3 that are targets for RdDM. {ECO:0000269|PubMed:21811420, ECO:0000269|PubMed:22064704, ECO:0000269|PubMed:23636332, ECO:0000269|PubMed:23637343}.
Cis-element ? help Back to Top
SourceLink
PlantRegMapPotri.001G189200.2
Regulation -- PlantRegMap ? help Back to Top
Source Upstream Regulator Target Gene
PlantRegMapRetrieve-
Annotation -- Nucleotide ? help Back to Top
Source Hit ID E-value Description
GenBankCU2314782e-55CU231478.1 Populus EST from mild drought-stressed leaves.
Annotation -- Protein ? help Back to Top
Source Hit ID E-value Description
RefseqXP_002299736.11e-129protein SAWADEE HOMEODOMAIN HOMOLOG 1 isoform X1
SwissprotQ9XI474e-51SHH1_ARATH; Protein SAWADEE HOMEODOMAIN HOMOLOG 1
TrEMBLB9GGM11e-127B9GGM1_POPTR; Uncharacterized protein
STRINGPOPTR_0001s19000.11e-128(Populus trichocarpa)
Best hit in Arabidopsis thaliana ? help Back to Top
Hit ID E-value Description
AT3G18380.12e-31sequence-specific DNA binding transcription factors;sequence-specific DNA binding
Publications ? help Back to Top
  1. Liu J, et al.
    An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing.
    Cell Res., 2011. 21(12): p. 1691-700
    [PMID:22064704]
  2. Law JA, et al.
    Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1.
    Nature, 2013. 498(7454): p. 385-9
    [PMID:23636332]
  3. Ma L, et al.
    Angiosperms Are Unique among Land Plant Lineages in the Occurrence of Key Genes in the RNA-Directed DNA Methylation (RdDM) Pathway.
    Genome Biol Evol, 2015. 7(9): p. 2648-62
    [PMID:26338185]
  4. Wang F,Axtell MJ
    AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana.
    Plant J., 2017. 90(1): p. 37-47
    [PMID:28002617]